Methods for detecting organisms and enzymatic reactions using raman spectroscopy

ABSTRACT

The present disclosure provides systems for the rapid and sensitive detection of organisms and molecules in samples. Reactants that produce Raman-active products are used in combination with Raman light scattering. The present disclosure can also be used to measure enzyme-kinetics.

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

This application is a Continuation-In-Part of application Ser. No.11/580,845, filed Oct. 16, 2006, which claims priority to ProvisionalApplication No. 60/727,328, filed Oct. 17, 2005, and ProvisionalApplication No. 60/836,936, filed Aug. 11, 2006, which are incorporatedby reference in their entireties.

DESCRIPTION OF THE INVENTION

1. Field of the Invention

The present disclosure generally relates to the field of biologicaldiagnostic equipment and testing methods.

2. Background of the Invention

There are currently many areas needing systems to detect biologicalorganisms or components (e.g. proteins, DNA, or other genetic material).These areas include: food safety, medical and veterinary diagnostics,pathogen detection, forensics, and homeland security. Current detectionmethods include immunochemistry and molecular biology, and biologicaltechniques such as Polymerase Chain Reaction (PCR) and Ligase ChainReactions (LCR). These methods and techniques are often limited inaccuracy, specificity, and sensitivity. Moreover, such methods oftenrequire extensive sample preparation, such as the isolation andpurification of nucleic acids.

Specificity of detection methods can be enhanced by using immunologicaltechniques. For example, medical diagnostics use antibody-basedtechniques to provide specificity in the detection of biologicalcomponents of a sample. Antibodies developed to specific compounds areknown to have high affinity and specificity for these components.However, antibodies are difficult to detect and are typically chemicallymodified with labels or tags that enhance detection. Unfortunately,antibody detection is prone to interference from other material in thesample including the sample matrix, wash components, and other chemicaland biological agents. Moreover, current techniques lack sensitivity atlow concentrations or numbers of antibodies (i.e. low concentrations ornumbers of targeted biological components).

Raman light scattering techniques (Raman spectroscopy) have been used inthe past to detect specific chemical components. Raman scattering is abasic property of the interaction of light with molecules. When lighthits a molecule it can cause the atoms of the molecule to vibrate. Thisvibration will then change the energy of additional light scattered fromthe molecule. This scattered light has characteristics that aremeasurable and are unique to the structure of the vibrating molecule.Thus, a Raman spectrum can be used to uniquely identify a molecule.

Raman spectroscopy has several advantages over existing detectionmethods, including simple application and production of quantifiabledata. However, Raman spectroscopy by itself lacks specificity andsensitivity for the detection of biological organisms and components.Therefore, there is a need in the art for reagents and methods thatallow Raman spectroscopy to be used for detection of organisms andbiological components.

The present disclosure is directed to methods that use the combinationof Raman spectroscopy and biological labeling techniques to identify andquantify biological organisms and components with higher sensitivity andspecificity than prior art techniques.

SUMMARY OF THE INVENTION

One embodiment of the disclosure is a method for detecting the activityof at least one enzyme in a sample comprising:

-   -   a) preparing a mixture comprising the sample and:        -   i. (optionally) at least one aromatic compound;        -   ii. at least one amine-containing compound; and        -   iii. at least one electron-donating compound;    -   b) incubating the mixture to form at least one Raman-active        product; and    -   c) detecting the at least one Raman-active product with Raman        spectroscopy.

In one embodiment, the at least one amine-containing compound is chosenfrom 4-aminoantipyrene and 5-aminosalicyclic acid.

In another embodiment, the at least one aromatic compound is chosen from2-hydroxybenzyl alcohol, 4-chloro-3,5-dimethylphenol, 2-naphthol,4-hydroxy-4-biphenyl-carboxylic acid, 5,7-dichloro-8-hydroxyquinoline,4-chloro-1-naphthol, phenol, and 4,5dihydroxy-naphthalene-2,7-disulfonic acid.

In another embodiment, the at least one amine-containing compoundcomprises:

wherein X is chosen from H, NH₂, Cl, Br, nitro, and benzyl, Y is chosenfrom H, Cl, Br, and nitro, and Z is chosen from H, benzyl, and NH₂. Inone embodiment, X is NH₂, and Y and Z are H. In another embodiment, X isCl, and Y and Z are H. In another embodiment, X is Br, and Y and Z areH. In another embodiment, X is nitro, and Y and Z are H. In anotherembodiment, X and Z are H and Y is Cl. In another embodiment, X and Zare H and Y is Br. In another embodiment, X and Z are H and Y is nitro.In another embodiment, X and Z are benzyl and Y is H. In anotherembodiment, X and Z are NH₂ and Y is H.

In another embodiment, the at least one amine-containing compoundcomprises:

wherein X is chosen from H, OH, Cl, Br, and nitro.

In another embodiment, the at least one amine-containing compoundcomprises:

wherein X is chosen from H, Cl, Br, and nitro.

In another embodiment, the at least one aromatic compound comprises:

wherein W, X, Y, and Z are chosen from H and OH. In one embodiment, Y isOH and X, Y and Z are H. In another embodiment, W is OH, and X, Y and Zare H. In another embodiment, W and X are OH, and Y and Z are H. Inanother embodiment, W and Y are OH, and X and Z are H. In anotherembodiment, W and Z are OH and X and Y are H.

In another embodiment, the at least one aromatic compound comprises:

wherein X, Y, and Z are chosen from H and OH. In one embodiment, X is OHand Y and Z are H. In another embodiment, X and Y are OH and Z is H. Inanother embodiment X and Z are OH and Y is H. In another embodiment, Zis OH and X and Y are H.

In another embodiment, the at least one aromatic compound comprises:

wherein X and Y are chosen from H and OH. In one embodiment X is OH andY is H. In another embodiment, X is H and Y is OH.

In another embodiment, the at least one aromatic compound comprises:

wherein X and Y are chosen from H and OH. In one embodiment, X is OH andY is H. In another embodiment, X is H and Y is OH.

In another embodiment, the at least one amine-containing compoundcomprises an aromatic amine. In another embodiment, the aromatic aminecomprises ortho-phenylenediamine, meta-phenylenediamine, orpara-phenyleneamine:

In another embodiment, the at least one electron-donating compound is ahydrogen peroxide. In another embodiment, the hydrogen peroxide ischosen from an aromatic hydrogen peroxide, urea hydrogen peroxide andhydrogen peroxide (H₂O₂). In another embodiment, the at least one enzymeis a peroxidase.

In another embodiment, the at least one aromatic compound is2-hydroxybenzyl alcohol, the at least one amine containing compound is5-aminosalicyclic acid, the at least one electron-donating compound isurea hydrogen peroxide, and the at least one enzyme is a peroxidase.

In another embodiment, the mixture is incubated in the presence of abase.

In another embodiment, the Raman spectroscopy is resonance Ramanspectroscopy.

Another embodiment is a method for detecting the activity of at leastone enzyme in a sample comprising:

-   -   a) preparing a mixture comprising the sample, 5-aminosalicyclic        acid, and a hydrogen peroxide chosen from an aromatic hydrogen        peroxide, urea hydrogen peroxide, and hydrogen peroxide H₂O₂;    -   b) incubating the mixture to form at least one Raman-active        product; and    -   c) detecting the at least one Raman-active product with Raman        spectroscopy.

In one embodiment, the mixture further comprises biotin.

Another embodiment is a method for detecting the activity of at leastone enzyme in a sample comprising:

-   -   a) preparing a mixture comprising the sample, an aromatic amine        comprising o-phenylenediamine, p-phenylenediamine, or        m-phenylenediamine, and a hydrogen peroxide chosen from an        aromatic hydrogen peroxide, urea hydrogen peroxide and H₂O₂;    -   b) incubating the mixture to form at least one Raman-active        product; and    -   c) detecting the at least one Raman-active product with Raman        spectroscopy.

Another embodiment is a method for detecting at least one target in asample comprising:

-   -   a) preparing a mixture comprising the target;    -   b) incubating the mixture with at least one ligand specific for        the target, wherein the at least one ligand comprises an enzyme;    -   c) providing to the mixture:        -   i. optionally, at least one amine-containing compound;        -   ii. at least one aromatic compound; and        -   iii. at least one electron-donating compound;    -   d) incubating the mixture to form at least one Raman-active        product; and    -   e) detecting the at least one Raman-active product with Raman        spectroscopy.

In one embodiment, the at least one amine-containing compound is chosenfrom 4-aminoantipyrene and 5-aminosalicyclic acid. In anotherembodiment, the at least one aromatic compound is chosen from2-hydroxybenzyl alcohol, 4-chloro-3,5-dimethylphenol, 2-naphthol,4-hydroxy-4-biphenyl-carboxylic acid, 5,7-dichloro-8-hydroxyquinoline,4-chloro-1-naphthol, phenol, and 4,5dihydroxy-naphthalene-2,7-disulfonic acid.

In another embodiment, the at least amine containing compound comprises:

wherein X is chosen from H, NH₂, Cl, Br, nitro, and benzyl, Y is chosenfrom H, Cl, Br, and nitro, and Z is chosen from H, benzyl, and NH₂. Inone embodiment, X is NH₂, and Y and Z are H. In another embodiment, X isCl, and Y and Z are H. In another embodiment, X is Br, and Y and Z areH. In another embodiment, X is nitro, and Y and Z are H. In anotherembodiment, X and Z are H and Y is Cl. In another embodiment, X and Zare H and Y is Br. In another embodiment, X and Z are H and Y is nitro.In another embodiment, X and Z are benzyl and Y is H. In anotherembodiment, X and Z are NH₂ and Y is H.

In another embodiment, the at least one amine-containing compoundcomprises:

wherein X is chosen from H, OH, Cl, Br, and nitro.

In another embodiment, the at least one amine-containing compoundcomprises:

wherein X is chosen from H, Cl, Br, and nitro.

In another embodiment, the at least one aromatic compound comprises:

wherein W, X, Y, and Z are chosen from H and OH. In one embodiment, Y isOH and X, Y and Z are H. In another embodiment, W is OH, and X, Y and Zare H. In another embodiment, W and X are OH, and Y and Z are H. Inanother embodiment, W and Y are OH, and X and Z are H. In anotherembodiment, W and Z are OH and X and Y are H.

In another embodiment, the at least one aromatic compound comprises:

wherein X, Y and Z are chosen from H and OH. In one embodiment, X is OHand Y and Z are H. In another embodiment, X and Y are OH and Z is H. Inanother embodiment X and Z are OH and Y is H. In another embodiment, Zis OH and X and Y are H.

In another embodiment, the at least one aromatic compound comprises:

wherein X and Y are chosen from H and OH. In one embodiment X is OH andY is H. In another embodiment, X is H and Y is OH.

In another embodiment, the at least one aromatic compound comprises:

wherein X and Y are chosen from H and OH. In one embodiment, X is OH andY is H. In another embodiment, X is H and Y is OH.

In another embodiment, the at least one amine-containing compoundcomprises an aromatic amine comprising ortho-phenylenediamine,meta-phenylenediamine, or para-phenyleneamine:

In another embodiment, the at least one electron-donating compound ischosen from an aromatic hydrogen peroxide, urea hydrogen peroxide andhydrogen peroxide (H₂O₂).

In another embodiment the enzyme is a peroxidase.

In another embodiment the at least one aromatic compound is2-hydroxybenzyl alcohol, the amine-containing compound is5-aminosalicyclic acid, the electron-donating compound is urea hydrogenperoxide, and the enzyme is a peroxidase.

In another embodiment, the mixture is incubated in the presence of abase.

In another embodiment, the Raman spectroscopy is resonance Ramanspectroscopy.

In another embodiment, the ligand is chosen from a receptor and anantibody. In another embodiment, the ligand is an antibody.

In another embodiment, the at least one target is an organism. Inanother embodiment, the organism is chosen from a bacteriophage, abacterium, including E. coli, Listeria, Salmonella, Vibrio,Camphelbacter, and Staphylococcus, and viruses such as HIV, Hepatitis,Adenovirus, Rhino virus, Human papilloma virus.

In another embodiment the target is a component of an organism. In oneembodiment, the component is a protein. In another embodiment, theprotein is an interleukin. In one embodiment, the interleukin is IL-2.In another embodiment, the protein is chosen from C-Reactive protein,Tumor Necrosis Factor Receptor II, and Human Cardiac Troponin I. Inanother embodiment, the target is a component of an organism chosen fromamino acids, nucleic acids, nucleotides, metabolites, carbohydrates,hormones, and metabolic intermediates.

Another embodiment is a method for detecting the activity of an enzymein a sample comprising:

-   -   a) preparing a mixture comprising the sample and:        -   i. optionally at least one aromatic compound;        -   ii. at least one amine-containing compound; and        -   iii. at least one electron-donating compound;    -   b) incubating the mixture to form at least one charge transfer        complex; and    -   c) detecting the at least one charge transfer complex with Raman        spectroscopy.

Another embodiment is a kit for detecting at least one enzyme activitycomprising:

a) (optionally) at least one aromatic compound;

b) at least one amine-containing compound;

c) at least one electron-donating compound; and

d) (optionally) suitable buffers for the at least one enzyme.

In one embodiment, the at least one amine-containing compound is chosenfrom 4-aminoantipyrene, 5-aminosalicyclic acid, and o-phenylenediamine;the at least one aromatic compound is chosen from 2-hydroxybenzylalcohol, 4-chloro-3,5-dimethylphenol, 2-naphthol,4-hydroxy-4-biphenyl-carboxylic acid, 5,7-dichloro-8-hydroxyquinoline,4-chloro-1-naphthol, phenol, and 4,5dihydroxy-naphthalene-2,7-disulfonic acid; and the at least oneelectron-donating compound is chosen from an organic hydrogen peroxide,urea hydrogen peroxide, and hydrogen peroxide (H₂O₂).

In another embodiment, the at least one amine-containing compoundcomprises:

wherein X is chosen from H, NH₂, Cl, Br, nitro, and benzyl, Y is chosenfrom H, Cl, Br, and nitro, and Z is chosen from H, benzyl, and NH₂. Inone embodiment, X is NH₂, and Y and Z are H. In another embodiment, X isCl, and Y and Z are H. In another embodiment, X is Br, and Y and Z areH. In another embodiment, X is nitro, and Y and Z are H. In anotherembodiment, X and Z are H and Y is Cl. In another embodiment, X and Zare H and Y is Br. In another embodiment, X and Z are H and Y is nitro.In another embodiment, X and Z are benzyl and Y is H. In anotherembodiment, X and Z are NH₂ and Y is H.

In another embodiment, the at least one amine-containing compoundcomprises:

wherein X is chosen from H, OH, Cl, Br, and nitro.

In another embodiment, the at least one amine-containing compoundcomprises:

wherein X is chosen from H, Cl, Br, and nitro.

In another embodiment, the at least one aromatic compound comprises:

wherein W, X, Y, and Z are chosen from H and OH. In one embodiment, Y isOH and X, Y and Z are H. In another embodiment, W is OH, and X, Y and Zare H. In another embodiment, W and X are OH, and Y and Z are H. Inanother embodiment, W and Y are OH, and X and Z are H. In anotherembodiment, W and Z are OH and X and Y are H.

In another embodiment, the at least one aromatic compound comprises:

wherein X, Y and Z are chosen from H and OH. In one embodiment, X is OHand Y and Z are H. In another embodiment, X and Y are OH and Z is H. Inanother embodiment X and Z are OH and Y is H.

In another embodiment, the at least one aromatic compound comprises:

wherein X and Y are chosen from H and OH. In one embodiment X is OH andY is H. In another embodiment, X is H and Y is OH.

In another embodiment, the at least one aromatic compound comprises:

wherein X and Y are chosen from H and OH. In one embodiment, X is OH andY is H. In another embodiment, X is H and Y is OH.

In another embodiment, the at least one amine-containing compoundcomprises an aromatic amine comprising ortho-phenylenediamine,meta-phenylenediamine, or para-phenyleneamine:

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of the patent or patent application publication with colordrawing(s) will be provided by the Office upon request and payment ofthe necessary fee.

FIG. 1 is a flow chart of a typical prior art immunoassay technique(ELISA) for the detection of biological organisms or components.

FIG. 2 is a diagram of an embodiment of the disclosed apparatus.

FIG. 3 is a flow chart of an embodiment of the disclosed technique forthe detection of biological organisms and/or components.

FIG. 4 is a block diagram of the enzyme system for converting chemicalcomponents to a Raman-active compound.

FIG. 5 is a flow chart of a technique for choosing laser lightfrequencies to excite specific target molecules.

FIG. 6 is an illustration of a micro-fluidic channel designed to detectRaman-active compounds.

FIG. 7 is an illustration of an array of micro-fluidic channels such asmight be incorporated into a custom integrated circuit.

FIG. 8 plots Raman spectra from an enzyme-linked immunoassay for apathogenic bacteria, Listeria, utilizing an antibody linked toperoxidase and with shift numbers (cm⁻¹) plotted on the abscissa andsignal magnitudes plotted on the ordinate (arbitrary units) for a samplecontaining Listeria (a) and a sample not containing Listeria (b).

FIG. 9 A plots Raman spectra measured at 3260 cm⁻¹ produced using RamanReagent formulation A-1 in three experiments, while FIG. 9 B plots SQRRaman spectra measured at 3500-4000 cm⁻¹ produced using Raman ReagentA-1 in the three experiments.

FIG. 10 plots Raman spectra measured at 3260 cm⁻¹ produced using RamanReagent A-1 (diamonds), and Raman Reagent A-2 (triangles) and A-3(squares).

FIG. 11 plots SQR Raman spectra measured at 3500-4000 cm⁻¹ producedusing Raman Reagent formulation A-1 (diamonds), and Raman Reagent A-2(squares and triangles).

FIG. 12 plots Raman spectra measured at 3260 cm⁻¹ produced using RamanReagent formulation A-2 (squares) and A-2 with fresh HPRO in BSA diluent(diamonds).

FIG. 13 plots Raman spectra measured at 3260 cm⁻¹ produced using RamanReagent B-1 (diamonds), B-2 (squares), B-3 (triangles), and B-4 (“Xs”).

FIG. 14 plots Raman spectra measured at 3260 cm⁻¹ produced using RamanReagent B-2 (squares) and B-2 with fresh HPRO in BSA diluent (diamonds).

FIG. 15 A plots Raman spectra measured at 3260 cm⁻¹ produced using RamanReagent C-1 while FIG. 15 B plots the corresponding SQR Raman spectrameasured at 3500-4000 cm⁻¹.

FIG. 16 A plots Raman spectra measured at 3260 cm⁻¹ produced using RamanReagent D-1 while FIG. 17 B plots the corresponding SQR Raman spectrameasured at 3500-4000 cm⁻¹.

FIG. 17 plots SQR Raman spectra measured at 3500-4000 cm⁻¹ producedusing Biotin-ASA-UP and ASA-UP.

FIG. 18 is a bar graph showing the relative sensitivity of the reagentstested.

FIG. 19 is a plot of the SQR Raman spectra measured at 3500-4000 cm⁻¹and absorbance spectrum measured at 450 nm in IL-2 immunoassays usingBASH-UP and TMB.

FIG. 20 A is a plot of an absorbance spectrum for a BASH-UP reaction,while FIG. 20 B is an absorbance spectrum for an OPD reaction.

FIGS. 21 A and 21 B are plots of fluorescence spectra of BASH-UPreactions without peroxidase, and FIGS. 21C and 21 D are plots offluorescence spectra of BASH-UP reactions with peroxidase.

FIGS. 22 A and 22 B are plots of fluorescence spectra of OPD reactionswithout peroxidase, and FIGS. 22 C and 22 D are plots of fluorescencespectra of OPD reactions with peroxidase.

FIGS. 23 A and 23 B are plots of Raman signals produced by BASH-UP andOPD reactions, respectively.

FIG. 24 A is a plot of Raman signals over time for an OPD reactionwithout peroxidase, and FIGS. 24 A-D are plots of Raman signals overtime for OPD reactions with decreasing amounts of peroxidase.

FIGS. 25 A-E are plots of SQR spectra over time for OPD reactions.

DETAILED DESCRIPTION OF THE INVENTION

Areas such as food safety, medical diagnostics, veterinary diagnostics,pathogen detection, forensics, and homeland security require the rapidand specific identification of biological organisms, such ascontaminating bacteria, and biological components such as proteins, DNA,or other genetic material. Of particular need in the art are rapid andsensitive methods for detecting bacteria.

A common assay to identify a bacterium in a sample is an immunoassay,which relies on detecting an antibody bound to the bacterium. Typically,the antibody is labeled and the presence of the antibody is detected byassaying for the presence of the label. Alternatively the antibody isconjugated to an enzyme, and the presence of the antibody-enzymeconjugate is detected by assaying for enzymatic activity. A commonlyused assay that employs an enzyme-antibody conjugate is the enzymelinked immunosorbant assay (ELISA). In standard assays, enzymaticactivity can be measured by incubating the enzyme-antibody conjugate inthe presence of reactants that are converted by the enzyme into productswhich can be detected through colorimetric, fluorogenic, andchemiluminescent means.

However, detection by colorimetric, fluorogenic, and chemiluminescentmeans suffers from several deficiencies such as limited dynamic range,limited sensitivity, and interference from background.

While Raman spectroscopy has several advantages over these methods, itgenerally cannot be used in combination with commonly used calorimetric,fluorogenic, and chemiluminescent reagents because they typically do notproduce useful Raman spectra. For example, the colorimetric reagents3,3′,5,5′-tetramethylene benzidine (TMB), andazinobisethlybenzthiazolinesulfonic acid (ABTS) do not produce Ramanspectra useful for detecting organisms. Accordingly, reagents thatproduce Raman-active products useful for detecting organisms aredesired, including reagents that can be used in immunoassay formatsemploying enzyme-antibody conjugates.

Reagents useful for detecting a bacterium in an immunoassay format usingRaman spectroscopy have certain desired characteristics. First, thereagents should produce a Raman signal in an area of the Raman spectrumthat does not already have background signal produced by the bacterium.Second, the Raman signal produced by the reagents should bequantifiable, allowing for detection over a wide range ofconcentrations.

The present disclosure is based in part on the discovery that certainamine-containing compounds can be used in immunoassay formats to detectorganisms and components, such as nucleic acids and proteins. Thesereagents are enzymatically converted to produce iminoquinone or otherproducts that have Raman signals at spectral regions not alreadycontaining Raman signals from the bacterium. Detection of the Ramansignals indicates the presence of the enzyme. When the enzyme is part ofan antibody-conjugate used in an ELISA assay, detection of Raman signalsindicates the presence of the target of the ELISA. Alternatively,Raman-active reagents can be incubated with enzymes that convert thesereagents into products with Raman spectra that differ from the reagents.The change in the Raman signal indicates the presence of the enzyme.Accordingly, use of these reagents allows for the rapid, specific andquantitative detection of enzymatic activity.

The present disclosure is also based in part on the discovery thatcertain combinations and amounts of the reagents of the disclosureproduce superior sensitivity. This sensitivity can be further enhancedthrough use of the Single Quantifiable Result (SQR) method of thedisclosure, which employs multiple wavenumber spectroscopic analyses.

The present disclosure is also based in part on the discovery that thecalorimetric reagent o-phenylenediamine (OPD) can be used to produceRaman-active products, in contrast to other colorimetric reagents. OPDcan be used in combination with Raman spectroscopy to measure real-timekinetics of enzyme activity.

While not being bound by any theory, it is believed that the presentdisclosure is based on the ability of certain compounds to formcharge-transfer complexes that can be detected by Raman spectroscopy.The presence of such complexes is supported by the discovery that thesecompounds produce broad Raman peaks consistent with formation of chargetransfer complexes. See, e.g., Rathore et al., “Direct Observation andStructural Characterization of the Encounter Complex in BimolecularElectron Transfers with Photoactivated Acceptors,” J. Am. Chem. Soc.119: 11468-11480 (1997). The discovery that certain compounds produceRaman-detectable charge transfer complexes provides a means to selectreactants that will produce such complexes.

DEFINITIONS

“Antibody”, as used herein, means an immunoglobulin or a part thereof,and encompasses any polypeptide comprising an antigen-binding siteregardless of the source, method of production, and othercharacteristics. The term includes for example, polyclonal, monoclonal,monospecific, polyspecific, humanized, single-chain, chimeric,synthetic, recombinant, hybrid, mutated, and CDR-grafted antibodies. Apart of an antibody can include any fragment which can still bindantigen, for example, an Fab, F(ab′)₂, Fv, scFv. The origin of theantibody is defined by the genomic sequence irrespective of the methodof production.

The terms “polypeptide,” “peptide,” and “protein,” are usedinterchangeably to refer to a polymeric form of amino acids of anylength, which can include naturally-occurring amino acids, coded andnon-coded amino acids, chemically or biochemically modified,derivatized, or designer amino acids, amino acid analogs,peptidomimetics, and depsipeptides, and polypeptides having modified,cyclic, bicyclic, depsicyclic, or depsibicyclic peptide backbones. Theterm includes single chain protein as well as multimers.

The term “amino acid” refers to monomeric forms of amino acids, whichcan include naturally-occurring amino acids, coded and non-coded aminoacids, chemically or biochemically modified, derivatized, or designeramino acids, amino acid analogs, peptidomimetics, and depsipeptides.

The terms “polynucleotide,” “nucleic acid,” “nucleic acid sequence,”“polynucleotide sequence,” and “nucleotide sequence” are usedinterchangeably herein to refer to polymeric forms of nucleotides of anylength. The polynucleotides can comprise deoxyribonucleotides,ribonucleotides, and/or their analogs or derivatives.

The term “nucleotide,” refers to monomeric nucleotides and includesdeoxyribonucleotides, ribonucleotides, and/or their analogs orderivatives.

The term “ligand” refers to a molecule that binds to another molecule,including a receptor.

Immunoassay Formats

The present disclosure can be practiced in various formats. In oneembodiment, the format is an immunoassay. In certain immunoassayembodiments, a target biologic is first bound to an antibody thatattached to a solid surface. Unbound components of the test sample arethen optionally washed away leaving only the bound biologic/antibodycombinations, which can be detected by Raman scattering of ultravioletlight.

In one embodiment, a combination of Raman spectroscopy and biologicallabeling techniques are used to identify and quantify biologicalcomponents, such as proteins or peptides including anypost-translational modifications, in specific conformations orconditions associated with disease: for example, prion proteins.

To increase the sensitivity an additional step is envisioned where oneor more new reactants are then introduced and become bound to thebiologic/antibody combination. The combination of the new reactant(s)with the biologic/antibody combination can now be detected using Ramanscattering of light. Examples of such reactants include, but are notlimited to the reagents listed in Table 1.

TABLE 1 Sensitivity Enhancing Reagents 1. antibodies labeled withRaman-active molecules; 2. enzyme/antibody conjugates combined withadditional chemical reactants that react to form Raman-active molecules;3. Raman-active reactants that chemically interact with the biologic;and 4. chemical reactants that are converted by the biologic intoRaman-active molecules.

It is also envisioned that instead of starting with a biologic/antibodycombination, the Raman detection methods can use chemicals that interactwith the biologic without the antibody.

The Raman-based methods can be applied to many immunoassays including,but not limited to, the detection of Human IL-11, Rat-C ReactiveProtein, Soluble Tumor Necrosis Factor Receptor II, and Human CardiacTroponin I.

The Raman-based methods can be applied to the detection of variety oforganisms and components. In one embodiment, bacteriophage are detected.In another embodiment, bacteria, including E. coli, Listeria,Salmonella, Vibrio, Camphelbacter, and Staphylococcus and detected. Inanother embodiment, viruses such as HIV, Hepatitis, Adenovirus, Rhinovirus, Human papilloma virus are detected. In another embodimentcomponents, including proteins, amino acids, nucleic acids, nucleotides,metabolites, hormones, and metabolic intermediates are detected.

It is also envisioned that specific binding partners or ligands for thetarget biologic other than antibodies may be used, for example, abiological receptor (a protein).

Although many of the techniques disclosed herein are associated with thedetection of biological organisms and components, the disclosure isapplicable to the detection of inorganic components, organic components,contaminants, or toxins in a sample. The disclosed detection techniquescan be enhance by using reactants that exhibit resonance Raman lightscattering. For certain reactants, there are frequencies of scatteredlight that are more intense which are specific to the structure of thesereactants. The resonance phenomena in certain embodiments of the presentdisclosure is solely related to the chemical structure and interactionof the target molecule, and not to any solid surface interaction such asfound in the technique known as Surface Enhanced Resonance RamanScattering (SERRS).

Single Quantifiable Result (SOR)

Raman spectra can be analyzed by obtaining a Single Quantifiable Result(SQR). The SQR number is the difference between a Raman spectracorresponding to a targeted analyte measured in a sample, and anybackground Raman signal/spectra observed in the measurement process. Thesteps of the SQR process are shown in Table 2.

TABLE 2 SQR Procedure 1) Optionally, spectra for the background of thesample (Negative Control) and for the samples being investigated (TestSamples) are measured. 2) The Raman values for a range of wave numbers,such as every 2nd wave number, or for every wave number, for theNegative Control and Test Samples are measured. 3) The differencebetween the Raman value for the Test Sample and the Negative Control isdetermined for each wave number measured and the sum of these values iscalculated (“Sum of the Differences”). 4) The difference between eachRaman value for the Test Sample and the Negative Control is squared andthe sum of these values is alculated (“Sum of the Squares of theDifferences”). 5) The square root of the “Sum of the Squares of theDifferences” is calculated (“Square Root of the Sum of the Squares ofthe Differences”). This value is designated as the SQR value.

The SQR process can include an assessment of whether the Raman signalsfrom the sample and background are appropriate (i.e. “valid”) andsufficient to indicate the presence of the targeted analyte in thesample (i.e. “positive value”). The SQR process may be performedmanually or with designed computer software. The Raman signals formultiple wave numbers are tabulated for the background and test spectra.In one embodiment, every 2^(nd) wave number is tabulated for both thebackground and test spectra. In another embodiment, every wave number istabulated for both the background and test spectra. In one embodimentthe range of wave numbers is from 2,000 to 4,000 cm⁻¹. In anotherembodiment, the range of wave numbers is from 3500 to 4000 cm⁻¹. Thedifference between the test signal and background signal is determinedfor a range of wave numbers and the square of this difference is stored.The sum of the squares is determined, and the square root of this sum isthe SQR value.

When using SQR, its validity can be verified by ensuring that thenegative and/or sample run is run appropriately (no systematic errorresulting in an incorrect assay), so that the Raman spectra has theintended meaning. If a background measurement is used, the backgroundsample must be representative of the background signal in the testsamples, and not due to random signal such as signal obtained when Ramanreadings are taken without a sample tube in the instrument. Samplespectra must not consistently run below (less than) that of the negativecontrol. Mathematically, the difference between a lower running sampleand the background would be transformed into a positive value, andpotentially interpreted as a “positive” SQR signal.

The following “Validity” analysis can be performed. The Raman value ofthe background sample (“Negative Control”) at a wave number, forexample, 3260 cm⁻¹ should run as expected (above a minimum and below amaximum value). This determination will aid in ensuring that a correctsample was run as the negative control, and that the assay was runcorrectly. The SQR value of the positive control should not run below anexpected value. This will aid in ensuring that a correct sample was runas the positive control, and that the assay was run correctly. The “Sumof the Differences” for each test sample should not run below anexpected value. These analyses help to ensure that the sample spectrumis not consistently running below (less than) that of the negativecontrol. The expected minimum and maximum values can be determinedempirically by establishing minima and maxima from values obtained inrepeated experiments.

The SQR method can be carried out manually or with the aid of acomputer. One embodiment of the disclosure is a computer bearing machineoperable language for the calculation of the SQR.

Instrumentation

It is also envisioned that embodiments of the present disclosure can beimplemented on a micro-fluidic channel (or well) integrated circuitusing micro or nano-fabrication technology in which the binding partneris immobilized in one or more micro-fluidic channels in a customintegrated circuitry which would also include the laser(s) and detectorsfor Raman spectroscopy. Such an implementation could detect singlebiological components such as pathological bacteria, proteins or geneticmaterial.

Thus an object of certain embodiments of the present disclosure is tohave a system for the detection of target biological organisms ofcomponents that utilizes a combination of chemical interactionsincluding binding with a final step of Raman light scattering.

Another object of certain embodiments of the present disclosure is tohave a system for the detection of target inorganic or organiccomponents that utilizes a combination of chemical interactionsincluding binding with a final step of Raman light scattering.

Another object of certain embodiments of the present disclosure is tocombine an immunoassay with detection using Raman light scattering.

Still another object of certain embodiments of the present disclosure isto increase sensitivity of detection by the use of chemical reactantsthat produce resonance Raman light scattering.

Yet another object of certain embodiments of the present disclosure isto have an integrated circuit design with micro-fluidic channels orwells which can perform the combination of binding and Raman lightscattering measurements.

These and other objects and advantages of the present disclosure willbecome obvious to a person of ordinary skill in this art upon reading ofthis disclosure including the associated drawings.

FIG. 1 is a flow chart of a typical prior art immunoassay technique(ELISA) (10) for the detection of biological organisms or components.The process begins by step (11) of preparing the liquid sample thatincludes the target biologic. For example, the sample can be prepared bypre-enrichment in a growth medium such as half-Frasier's broth or othersuitable microbial growth medium. Alternately, a liquid sample fortesting may be obtained from any liquid source. Solid material may beimmersed in an appropriate liquid solution and potential target organismor molecules placed in solution and then sampled in the liquid. In thenext step (12) the prepared liquid sample is combined (or mixed) with abinding partner that has been attached to a solid surface. Typicalbinding partners include antibodies, bacteriophage, and bacteriophageproteins. For example plastic microtiter plates, latex beads or magneticmicroparticles may be used. Other solid supports such as nitrocellulose,filter paper, nylon and other plastics may also be used. Theantibody/biologic combination is then incubated in step (13) to allowtime for the biologic and antibody to bind together. Once this hasoccurred the combined binding partner/biologic is decanted (poured off)and washed to remove unbound biologics and other unwanted materials. Newreactants are added in step (15) to enhance the sensitivity of themixture to detection of signal molecules by various methods. Examples ofsuch reactants include those listed in Table 3.

TABLE 3 Sensitivity Enhancing Reagents 1. binding partners labeled withradioactive molecules 2. binding partners labeled with fluorescentmolecules 3. enzyme/binding partner conjugates combined with additionalchemical reactants that react to form light absorbing molecules 4.enzyme/binding partner conjugates combined with additional chemicalreactants that react to form light producing molecules 5. enzyme/bindingpartner conjugates combined with additional chemical reactants thatreact to form light reflecting molecules

The mixture containing the bound binding partner/biologic and newreactants is the incubated in step (13) to allow time for the reactionto occur. At this point in many cases, the reaction part of the process(10) is complete and step (16) of measuring the molecules produced orincluded in steps (11) through (15) inclusive can be performed. Ifadditional reactants are required, steps (14), (15) and (13) may berepeated one or more times in succession until the appropriate signalmolecules are present.

The measurement of the signal molecule(s) provides a quantitative resultthat can then be analyzed and compared in step (17) to a known set ofcalibrated responses of known concentrations of the target biologic.This comparison results in step (18) which is the quantified result andassociated report of the concentration of the target biologic in thesample prepared in step (11).

Although the descriptions of the process (10) of FIG. 1 have beenassociated with the detection of a biological organism or component, theprocess (10) is also applicable to the detection of many types ofmolecules to which antibodies or other binding partners can react.

FIG. 2 is a diagram of an embodiment of the present disclosure detectionsub-system (20). A laser (21) produces a laser beam (22) which isfocused by the focusing optics (23) into a focused laser beam (24) whichhits the target sample (25). The backscattered light (26) from thesample (25) is focused into the beam (28) by the focusing optics (27).The beam (28) is directed into the spectrometer (30) with detector (31).The output from the detector (31) is the signal (32) which is receivedby the personal computer (40) for analysis, storage and/or printing withthe printer (42). The laser (21) is typically a continuous wavelength(CW) laser with output in the visible range. For example, an argon ionlaser, helium neon laser, argon ion laser pumped tunable dye laser, or adiode laser in the green, red or other frequency. Focusing optics (23)and (27) include mirrors, lenses, irises, shutters, diffractiongratings, and/or polarizers. The target sample (25) may be liquid, gasor solid and in certain embodiments, the target sample would use aliquid or precipitated solid. The spectrometer (30) spatially separatesthe scattered light based on wavelength. An example of a usablespectrometer for the present disclosure is the Lambda Solutions modelPS-1. The detector (31) measures the amplitude of the light spatiallyseparated by the spectrometer (30) and converts this into an electricalsignal (analog or digital). In certain embodiments, the detector wouldprovide the electrical signal using a standardized computer interfacesuch as RS-232, USB, parallel, IEEE 1394. An example of a usabledetector (30) for the present disclosure is a Lambda Solutions PS-1. Thepersonal computer (40) can be any desktop or laptop PC with anappropriate interface to the detector (31) and software designed toanalyze, store and/or print the spectrum of the backscattered light (26)received by the spectrometer (30).

FIG. 3 is a flow chart of an embodiment of the present disclosure (30)for the detection of biological organisms and/or components. The processbegins by step (31) of preparing the liquid sample that includes thetarget biologic. For example, the sample may be prepared bypre-enrichment in a growth medium such as half-Frasier's broth or othersuitable microbial growth medium. Alternately, a liquid sample fortesting may be obtained from any liquid source. Solid material may beimmersed in an appropriate liquid solution and potential target organismor molecules placed in solution and then sampled in the liquid. In thenext step (32), the prepared liquid sample is combined (or mixed) withan antibody that has been attached to a solid surface. For example,plastic microtiter plates, latex beads or magnetic microparticles may beused. The antibody/biologic combination is then incubated in step (33)to allow time for the biologic and antibody to bind together. Once thishas occurred the combined antibody/biologic is decanted (poured off) andwashed to remove unbound biologics and other unwanted materials. Newreactants are added in step (35) to enhance the sensitivity of themixture to detection by Raman light scattering. Examples of suchreactants are listed in Table 1.

The mixture containing the bound antibody/biologic and new reactants isthe incubated in step (33) to allow time for the reaction to occur. Atthis point in many cases, the reaction part of the process (30) iscomplete and step (36) of measuring Raman light scattering fromRaman-active molecules produced by steps (31) through (35) inclusive canbe performed. If additional reactants are required, steps (34), (35) and(33) may be repeated one or more times in succession until theappropriate Raman-active molecules are present.

The measurement of Raman light scattering is a spectrum that can then beanalyzed and compared in step (37) to a known set of calibratedresponses of known concentrations of the target biologic. Thiscomparison results in step (38) which is the quantified result andassociated report of the concentration of the target biologic in thesample prepared in step (31).

Listeria may be measured in an (enzyme-linked immunosorbant assay) ELISAformat. 100 microliters of various-concentrations of bacteria; 100,000,50,000, 25,000, 12,500, 6,250 and 0 colony forming units (cfu) per mlare added to microwells coated with anti-Listeria antibodies. After anincubation period between 30 and 60 minutes at 37° C., the wells aredecanted and washed with a mild detergent solution three times. 100 μlof peroxidase-conjugated anti-Listeria antibodies are added to the welland incubated for 1 to 4 hours at 37° C. The wells are decanted andwashed with a mild detergent solution three times. A mixture of4-hydroxylbenzyl alcohol (80.6 mM), 4-aminoantipyrene (24 mM),Urea-Hydrogen Peroxide (10.6 mM) in 125 mM MES buffer (pH 6.0) is addedand color is allowed to develop for 30-60 minutes. Raman Spectra ofdeveloped color from each well are developed and responses quantified.

Although the descriptions of the process (30) of FIG. 3 have beenassociated with the detection of a biological organism or component, theprocess (30) is also applicable to the detection of inorganic or organicmolecules, contaminants or toxins.

FIG. 4 is a block diagram for a chemical conversion system (40) whichuses an enzyme for converting chemical components to a Raman-activecompound. For example, one or more reactants designated (41), (42) and(43) are mixed with a biological catalyst (44). The biological catalyst(44) may be an enzyme specific for metabolizing the reactants providedor RNA structures designed to interact with the one or more reactants(41), (42), and (43). A conversion or combination of the reactantsoccurs in the reaction (45) and a measurable product (46) is formed. Forexample, the reactants and those in Table 4 are mixed together in thepresence of peroxidase (44) and urea hydrogen peroxide (UP) (43).

TABLE 4 Reactants Producing Raman-active Products 2-hydroxybenzylalcohol (HBA) (41) 5-aminosalicyclic acid (ASA) (42)4-chloro-3,5-dimethylphenol (CDMP) (41) 5-aminosalicyclic acid (ASA)(42) 2-naphthol (NAP) (41) 5-aminosalicyclic acid (ASA) (42)4-hydroxy-4-biphenyl-carboxylic acid (HBCA) (41) 5-aminosalicyclic acid(ASA) (42) 5,7 dichloro-8-hydroxyquinoline (DHQ) (41) 5-aminosalicyclicacid (ASA) (42) 4-chloro-1-naphthol (41) 4-aminoantipyrene (42) phenol(41) 4-aminoantipyrene (42)

When mixed together, these components will yield an iminoquinonecompound which is detectable using Raman spectroscopy. A reaction usingHBA, ASA and UP is referred to as BASH-UP.

Additional reactants that may produce Raman-active products can be usedin the disclosed methods, such as compounds comprising a least onehydroxyl group and one amino group at positions 1 and 4 in a benzene ornaphthalene. Inclusion of additional groups such as carboxyl, amine,chlorine, bromine, nitro and other functional groups may enhance theRaman signal. Such compounds include:

wherein X is chosen from H, NH₂, Cl, Br, nitro, and benzyl, Y is chosenfrom H, Cl, Br, and nitro, and Z is chosen from H, benzyl, and NH₂. Inone embodiment, X is NH₂, and Y and Z are H. In another embodiment, X isCl, and Y and Z are H. In another embodiment, X is Br, and Y and Z areH. In another embodiment, X is nitro, and Y and Z are H. In anotherembodiment, X and Z are H and Y is Cl. In another embodiment, X and Zare H and Y is Br. In another embodiment, X and Z are H and Y is nitro.In another embodiment, X and Z are benzyl and Y is H. In anotherembodiment, X and Z are NH₂ and Y is H.

Such compounds also include:

wherein X is chosen from H, OH, Cl, Br, and nitro.

Such compounds also include:

wherein X is chosen from H, Cl, Br, and nitro.

Additional compounds that may produce Raman-active products in thedisclosed methods include compounds comprising at least two hydroxylfunctions in 1, 2 or 1, 4 positions in a benzene or naphthalene ring.

Such compounds include:

wherein W, X, Y, and Z are chosen from H and OH. In one embodiment, Y isOH and X, Y and Z are H. In another embodiment, W is OH, and X, Y and Zare H. In another embodiment, W and X are OH, and Y and Z are H. Inanother embodiment, W and Y are OH, and X and Z are H. In anotherembodiment, W and Z are OH and X and Y are H.

Such compounds include polyphenols, such as:

wherein X, Y and Z are chosen from H and OH. In one embodiment, X is OHand Y and Z are H. In another embodiment, X and Y are OH and Z is H. Inanother embodiment X and Z are OH and Y is H. In another embodiment, Zis OH and X and Y are H.

Additional compounds that may produce Raman-active products in thedisclosed methods include compounds comprising hydroxymethylene (—CH₂OH)group in a benzene or naphthalene. Inclusion of additional hydroxylgroups at positions 1, 4, and 6 may enhance the Raman signal.

Such compounds include:

wherein X and Y are chosen from H and OH. In one embodiment X is OH andY is H. In another embodiment, X is H and Y is OH.

Such compounds also include:

wherein X and Y are chosen from H and OH. In one embodiment, X is OH andY is H. In another embodiment, X is H and Y is OH.

Such compounds also include aromatic amines, including compoundscomprising ortho-phenylenediamine, meta-phenylenediamine, andpara-phenyleneamine:

Such compounds also include 2,4-diaminobenzyl alcohol,2-amino-1-naphthol, and 4-aminoantipyrene.

The product of the reaction (45) may be used as a quantitative orqualitative reporting molecule for the reaction and as such may be usedas a probe for the presence of specific biological targets if conjoinedwith, for example, specific antibodies or biological or chemical bindingpartners.

FIG. 5 is a flow chart of the technique (50) for choosing one or morelaser light frequencies to excite specific target molecules forresonance Raman detection. A Raman-active product (51), such as theproduct (46) produced by the reaction (45) of FIG. 4, is a chemical thatpossesses a structure which is Raman-active. The absorbance spectrum ofthe product (51), is measured in step (52) using a technique such asabsorbance or transmittance spectrophotometry. In step (53), one or morewavelengths are identified at which the product (51) absorbs light asseen in the spectrum measured in step (52). In step (54), a laser thatemits light at a wavelength corresponding to one of the one or morewavelengths identified in step (53) is then selected. Such laserwavelengths can be in the visible range, ultra-violet range or infra-redrange. For example, for the Listeria detection reaction (30) describedfor FIG. 3, the laser wavelength selected is 532 nm.

Finally, in step (55) the laser chosen in step (54) is used to irradiatethe Raman-active product created in step (51). This will confirm thatthere is significant Raman scattering of the Raman-active productcreated in step (51) to provide adequate signal for detection.

FIG. 6 is an illustration of a micro-fluidic channel (60) designed todetect Raman-active compounds. A source liquid (or gas) sample (61)including the target biological organisms or components flows throughthe channel (62). The target biological organisms or components willreact and be bound to the reactant(s) attached to the active surface(64). Light (68) from the laser (65) produces Raman scattered light (69)which is detected by the photodetector (66). The photodetector isdesigned to measure one or more specific wavelengths which correspond tothe Raman spectrum of the combined reactant(s) and biological organismor component. It is also envisioned that instead of binding thebiological organism or component to the surface (64), the reactant(s)may be released from the surface and the Raman-scattering laser (65) anddetector (66) may be located downstream from the surface.

FIG. 7 is an illustration of an array of micro-fluidic channels (70)designed to detect Raman-active compounds. One or more source liquid (orgas) samples (71A), (71B) through (71N) which include the targetbiological organisms or components flow through the channels (72A),(72B) through (72N). The target biological organisms or components willreact and be bound to the reactant(s) attached to the active surfaces(74A), (74B) through (74N). Light, (78A) through (78N), from the lasers,(75A) through (75N), produce Raman-scattered light, (79A) through (79N),which is detected by the photodetectors (76A) through (76N). Thephotodetectors are designed to measure one or more specific wavelengthswhich correspond to the Raman spectrum of the combined reactant(s) andbiological organisms or components bound to the surfaces.

The number of micro-fluidic channels in the array of micro-fluidicchannels as limited by the upperbound N, ranges from 2 to 100,000. It isalso envisioned that a multiplicity of different reactants and laserwavelengths may be used in different channels. This would allowdetection of multiple wavelengths of scattering from the same biologicalorganism or component or it would allow the simultaneous detection ofmultiple different biological organisms and components. Finally insteadof an array of micro-fluidic channels (70), it is envisioned that anarray of micro-fluidic wells could be used to produce a 2-dimensionalarray of Raman-scattering detectors.

The present disclosure is more particularly described in the followingexamples that are intended as illustrative only since numerousmodifications and variations therein will be apparent to those skilledin the art. Various embodiments are now described in detail. As used inthe description and throughout the claims that follow, the meaning of“a”, “an”, and “the” includes plural reference unless the contextclearly dictates otherwise. Also, as used in the description andthroughout the claims that follow, the meaning of “in” includes “in” and“on” unless the context clearly dictates otherwise. All references citedand discussed in this specification are incorporated herein by referencein their entireties and to the same extent as if each reference wasindividually incorporated by reference.

EXAMPLES Example 1 Detection of Listeria Using BASH-UP

FIG. 8 depicts Raman spectra obtained from an enzyme-linked immunoassayfor the pathogenic bacteria Listeria utilizing the two-component BASH-UPchemistry, an enzyme-linked antibody, and Raman detection proceduredescribed below utilizing the following buffers and reagents:

Working Saline Buffer (used for washes in protocol):

10 mM Sodium Phosphate, pH 6.0

137 mM Sodium Chloride

2.67 mM Potassium Chloride

0.09 mM Ethylenediaminetetraacetic acid (EDTA)

0.05% Bronidox-L

Final Chemistry Reagent (BASH):

0.588 mM 5-Aminosalicylic Acid

0.145 mM 2-Hydroxybenzyl alcohol

0.005 mM L-Ascorbic Acid

0.09% Tween-20

UP Component:

1.063 mM Urea Peroxide

Working Saline Buffer

Additional Reagents:

-   -   1. Microparticles—Anti-Listeria (antibody) coated magnetic        microparticles at 2 million microparticles/sample upon addition.    -   2. Conjugate Solution—Anti-Listeria (antibody) conjugated with        Horseradish Peroxidase (HRPO) at 2 μg/sample upon addition

Samples of either heat-killed Listeria or a negative broth (1 ml) weresubject to the following procedure. Note, the 1 ml sample may be fromculture, control, swab, sponge, etc.

Procedure:

1. Add 100 μl of microparticles to sample.

2. Incubate 30 minutes at room temperature.

3. Capture microparticles with magnet 10 minutes.

4. Remove sample volume.

5. Add 500 μl Working Saline Buffer, mix 2 minutes at 1000 rpm.

6. Capture microparticles with magnet 2 minutes.

7. Remove wash volume.

8. Repeat steps 3-7 two more times for a total of 3 washes.

9. Add 200 μl Conjugate Solution.

10. Mix solution for 30 minutes.

11. Repeat wash steps 3-7 for a total of 3 washes.

12. Add 200 μl Final Chemistry Reagent.

13. Incubate 20 minutes with mixing at 1000 rpm.

14. Add 40 μl 0.5 N NaOH.

15. Mix 2 minutes at 1000 rpm.

16. Capture microparticles with magnet 2 minutes.

17. Transfer volume to cuvette for Raman signal detection.

In this procedure, the Final Chemistry Reagent was a two componentBASH-UP chemistry. The Raman signal was generally stable for ˜1 hour orlonger. The first component in the chemistry (BASH) contained 2-hydroxybenzyl alcohol (0.02 mg/ml), 5-amino salicylic acid (0.1 mg/ml), 0.1%Tween-20, and ascorbic acid (1 μg/ml) in the Working Saline Buffer (pH6.0). The second component (UP) contained urea peroxide adduct (1 mg/ml)the working Saline Buffer (pH 6.0) including EDTA (1 mM). Theseformulations maintained activity when refrigerated out of direct lightfor more than one month. Mixing the two components at a ratio of 1 UP to10 BASH created a working solution of BASH-UP that was generally stablefor one working day.

An aliquot of BASH-UP was added to samples containing either heat-killedListeria or a negative broth and allowed to react for 30 minutes. Theappropriate period of time will vary based on the sensitivity ofdetection required. 40 μl of 0.5 N NaOH was added to the 200 μl BASH-UPreaction volume to stop the reaction and render the productsRaman-detectable. Alteration of the volume and concentration of the NaOHmay afford greater signal stability as required by the particular assay.

Raman scattering was observed from the 240 μl sample using a RamanSystems R-3000 Raman spectrometer with a 532 nm laser operated at thehigh power setting.

Example 2 Colorimetric Assays of Horseradish Peroxidase (HRPO)

Colorimetric assays of Horseradish Peroxidase (HRPO) activity wereconducted to obtain data that could be compared with the Raman-basedmethods. TMB develops a deep blue soluble product when reacted withhorseradish peroxidase. ABTS develops a blue-green product when reactedwith horseradish peroxidase.

Colorimetric assays were performed with the TMB and ABTS reactions usingtwo different methods:

Method A (TMB): HRPO dilutions were made to measure 1000 pg to 0.0125 pgper 50 μl sample in phosphate-buffered saline (PBS) containing 0.1%bovine serum albumin (BSA) at pH 7.4. 50 μl HRPO sample per dilution wasadded to 200 μl TMB reagent and allowed to react for 15 or 30 minutes atwhich time 200 μl stop-solution (KPL Laboratories) was added. Absorbancewas measured at 450 nm for each sample.

Method B (ABTS): HRPO dilutions were made to allow 1000 pg to 0.0125 pgper 50 μl sample in PBS at pH 7.4. 50 μl HRPO sample per dilution wasadded to 200 μl ABTS reagent and allowed to react for 15 or 30 minutesat which time 200 μl stop solution (1% SDS in water) was added.Absorbance was measured at 405 nm for each sample.

The limit of detection of HRPO for TMB was 8 pg/ml and the dynamic rangewas 5 to 5000 pg/ml. For ABTS, the limit of detection was 32 pg/ml andthe dynamic range was 32 to 5000 pg/ml.

Example 3 Fluorogenic and Chemiluminescent Assays of HRPO

Several reagents were tested: Sigma Chemiluminescent PeroxidaseSubstrate, Pierce Fluorogenic (Chemifluorescent) Substrate Kit, AnaSpecSensolyte ADHP Fluorogenic Substrate, Invitrogen Molecular Probes AmplexRed Fluorogenic Substrate, and KPL Laboratories LumiGLO. Sigma andPierce substrates did not work with HRPO in PBS or with BSA-containingbuffer.

A. AnaSpec Fluorogenic ADHP Assay

AnaSpec Fluorogenic kit utilizes ADHP(10-acetyl-3,7-dihydroxyphenoxazine) to analyze peroxidase in solutionwhereby ADHP is oxidized in the presence of peroxidase and hydrogenperoxide. The oxidized product of ADHP (resozufin) gives pinkfluorescence that can be measured at the emission wavelength of 590 nmwith the excitation wavelength of 530-560 nm. An overdose of peroxidasein the assay will further convert the fluorescent resorufin tonon-fluorescent resozurin to yield reduced fluorescent signal. HRPOdilutions were made to allow detection of 1,000,000 pg to 0.0625 pg per50 μl sample were prepared in PBS at pH 7.4. The procedure was the sameas described earlier for TMB and ABTS assays, and two methods were used.

Method A: ADHP Reagent and Hydrogen Peroxide were prepared permanufacturer's instructions. 500 μl of peroxidase solution was added to500 μl ADHP reagent in a 1.5 ml plastic microcuvette. The reactionmixture was gently mixed, and incubated at room temperature for 30 minwithout light exposure. The fluorescent signal was measured for emissionat 590 nm with excitation at 550 nm on an Ocean Optics FluorescentSpectrometer.

Method B: Similar to Method A except 400 μl of each of peroxidase andADHP reagents were used.

The sensitivity (lowest limit of detection) of the AnaSpec ADHPfluorescent assay was found to be 12.5 pg/ml of HRPO. The assay rangewas linear from 250 pg/ml to 0 pg/ml of HRPO.

B. Molecular Probes-Invitrogen Amplex Red Fluorogenic Assay

Molecular Probes Fluorogenic assay kit employs Amplex Red(10-acetyl-3,7-dihydroxyphenoxazine), which is similar to AnaSpec ADHPassay. The oxidized end product of the assay with peroxidase andhydrogen peroxide is resorufin. The assay claim is 1×10−5 U/ml,equivalent to 10 pg/ml (1×10−5 ml).

HRPO dilutions made to allow detection of 1,000,000 pg to 0.0625 pg per50 μl sample were prepared in PBS, pH 7.4. Amplex Red Reagent andHydrogen Peroxide were prepared per Manufacturer's instructions. 400 μlof peroxidase solution was added to 400 μl ADHP reagent in a 1.5 mlplastic microcuvette. The reaction mixture was gently mixed andincubated at room temperature for 30 min in the dark. The fluorescentsignal was measured at 590 nm with excitation at 550 nm on an OceanOptics Fluorescent spectrometer at 30 min and 35 min.

The sensitivity (lowest limit of detection) of the Molecular ProbesAmplex Red Fluorescent assay was found to be 25 pg/ml of HRPO. The assayrange was linear from 250 pg/ml to 0 pg/ml of HRPO.

C. LumiGLO®

LumiGLO is a luminol-based chemiluminescent substrate designed for usewith peroxidase-labeled reporter molecules. In the presence of hydrogenperoxide, HRPO converts luminol to an excited intermediate dianion. Thisdianion emits light on return to its ground state. After reaction withHRPO conjugate, the light emission from LumiGLO reaches maximumintensity within 5 minutes and is sustained for approximately 1-2 hours.

The sensitivity (lowest limit of detection) of the LumiGLO inrepresentative experiments was found to be 11 pg/ml of HRPO.

Raman-Based Assays

A variety different combinations and amounts of reagents producingRaman-active products were tested to find the optimal reactionconditions for each. For these assays, 50 μl HRPO sample per dilutionwas added to 150 μl of the selected Raman Reagent (A-E), plus ureaperoxidase in volume ratio of 9:1, and samples allowed to react for 30minutes. Formulations of Reagents A-E are shown in the tables below. 50μl of 0.5 N NaOH was then added to each sample which was allowed toincubate for 30 minutes. Raman-based assays were also performed in HRPOsamples diluted in PBS at pH 7.4. Raman spectra were recorded with aDiagnostics Raman Systems INC QE 65000 Raman Detector. Spectral analyseswere based on measurement of the Raman signal at wavelength 3260 cm⁻¹and by SQR using every 2^(nd) wavenumber between 3500 cm⁻¹ and 4000cm⁻¹.

Example 4 Raman Reagent A (BASH-UP)

The formulations used for this study are listed in Table 5:

TABLE 5 RAMAN REAGENT A ASA HBA AA Formula Buffer μg/ml μg/ml μg/ml A-1PBS-EDTA, pH 6.0 100 20 20 A-2 PBS-EDTA, pH 6.0 500 20 A-3 PBS-EDTA, pH6.0 100 100 A-4 PBS-EDTA, pH 6.0 300 20 A-UP PBS-EDTA, pH 6.0 1000

HRPO was reacted with Raman Reagent A-1 with dilution in PBS containing0.1% BSA at pH 7.4. Raman spectra were recorded for HRPO dilutions from0 (“blank”) to 100 pg/ml. FIG. 9 A shows the single peak (3260 cm⁻¹)dependence on HRPO concentration and FIG. 9 B shows the same resultsafter applying SQR analysis (3500-4000 cm⁻¹). Table 6 compares thedetection limits of HRPO detection from different experiments, showingincreased sensitivity from the SQR method compared to measurements basedon a single peak.

TABLE 6 DETECTION LIMITS Formulation Single peak SQR Increase insensitivity A-1 1.0 pg 0.5 pg 2 times A-1 2.5 pg 0.5 pg 5 times A-1 2.5pg 0.025 pg  10 times 

HRPO was reacted in Raman Reagents A-1, A-2, and A-3 and Raman spectrawere recorded for HRPO dilutions from 0 (“blank”) 5 pg/ml. FIG. 10 showsthe single peak (3260 cm⁻¹) dependence on HRPO concentration. FIG. 11shows an SQR analysis of Raman Reagents A-1 and A-2 (3500-4000 cm⁻¹).

HRPO was reacted with Raman Reagent A-2, and with fresh HPRO in BSAdiluent. FIG. 12 shows the single peak (3260 cm⁻¹) dependence on HRPOconcentration.

Table 7 compares the detection limits from different Raman Reagent Aformulations, showing the increase in sensitivity provided by the SQRmethod.

TABLE 7 DETECTION LIMITS Formulation Single peak SQR Increase insensitivity A-1 1 pg   0.5 pg 2-4 times  A-2 0.5 pg     0.05 pg 10 timesA-2* 0.25 pg   0.00625 pg 40 times A-1** 1 pg     1 pg No change *FreshHRPO in BSA diluent **A-1 lacking AA

Example 5 Raman Reagent B

Raman reagent formulations used for this study are listed in Table 8.

TABLE 8 RAMAN REAGENT B ASA CDMP Formula Buffer μg/ml μg/ml B-1PBS-EDTA, pH 6.0 100 50 B-2 PBS-EDTA, pH 6.0 500 25 B-3 PBS-EDTA, pH 6.0250 25 B-4 PBS-EDTA, pH 6.0 100 25 B-UP PBS-EDTA, pH 6.0 1000

HRPO was reacted in Raman Reagent B-1, B-2, B-3, and B-4. Raman spectrawere recorded for HRPO dilutions from 0 (“blank”) to 1000 pg/ml. FIG. 13show the single peak (3260 cm⁻¹) dependence on HRPO concentration. FIG.14 shows single peak dependence on HRPO concentration and compares freshHRPO in BSA diluent and formulation B-2

Table 9 compares the detection limits from several different Ramanreagent B formulations, showing the increase in sensitivity provided bythe SQR method.

TABLE 9 DETECTION LIMITS Formulation Single peak SQR Increase insensitivity B-1 5 pg 1 pg 5 times B-2 1 pg 0.5 2 times B-3 0.5 pg   0.05pg 10 times  B-3* 0.25 pg   0.00625 pg 40 times  B-4 1 pg 0.5 pg 5 times*Fresh HRPO in BSA diluent

Example 6 Raman Reagent C

Raman reagent formulations used for this study are listed in Table 10.

TABLE 10 RAMAN REAGENT C ASA NAP Formula Buffer μg/ml μg/ml C-1PBS-EDTA, pH 6.0 400 150 C-2 PBS-EDTA, pH 6.0 400 200 C-3 PBS-EDTA, pH6.0 400 100 C-UP PBS-EDTA, pH 6.0 1000

HRPO was reacted in Raman Reagent C-1. Spectra were recorded for HRPOdilutions from 0 (“blank”) to 1000 pg/ml. FIG. 15 A shows the singlepeak (3260 cm⁻¹) dependence on HRPO concentration and FIG. 15 B showsthe corresponding SQR spectra. Table 11 compares the detection limitsfor the single peak and SQR method, showing increased sensitivity fromSQR.

TABLE 11 DETECTION LIMITS Formulation Single peak SQR Increase insensitivity C-1 0.5 pg  0.1 pg 5 times C-3* 0.5 pg 0.25 pg 2 times*Fresh HRPO in BSA diluent

Example 7 Raman Reagent D

Raman reagent formulations used for this study are listed in Table 12.

TABLE 12 RAMAN REAGENT D ASA HBCA Formula Buffer μg/ml μg/ml D-1PBS-EDTA, pH 6.0 400 120 D-UP PBS-EDTA, pH 6.0 1000

HRPO was reacted in Raman Reagent D-1. Spectra were recorded for HRPOdilutions from 0 (“blank”) to 1000 pg/ml. FIG. 16 A shows the singlepeak (3260 cm⁻¹) dependence on HRPO concentration and FIG. 16 B showsthe corresponding SQR spectra.

TABLE 13 RAMAN REAGENT E ASA DHQ Formula Buffer μg/ml μg/ml E-1PBS-EDTA, pH 6.0 182 2270 E-2 PBS-EDTA, pH 6.0 360 91 E-UP PBS-EDTA, pH6.0 1000

HRPO was reacted in Raman Reagent D-1. The detection limit for RamanReagent formulation D was 50 pg/ml.

Example 8 Sensitivity Tests

Sensitivity tests of Peroxidase with different Raman Reagents were donein PBS at pH 7.4, containing BSA. The study was intended to evaluate thesensitivity in PBS without BSA. The following reagents were used in thisstudy:

Raman Reagent A-1: 500 μg/ml ASA; 20 μg/ml HBA; 20 μg/ml M

Raman Reagent B-3: 250 μg/ml ASA; 25 μg/ml CDMP

Raman Reagent C-1: 400 μg/ml ASA; 150 μg/ml NAP

HRPO dilutions made to allow 1000 pg to 0.0125 pg per 50 μl sample wereprepared in PBS at pH 7.4. 50 μl HRPO sample per dilution was added to150 μl reagent and allowed to react for 30 minutes. 50 μl of 0.5 N NaOHwas then added. After incubation for 30 minutes, Raman spectra wererecorded using a Sword Diagnostics Raman Systems INC QE 65000 RamanDetector. Data were analyzed using SQR. Results from representativeexperiments appear in Tables 14-18.

Example 9 Biotin-ASA-UP, ASA-UP and ASA-UP in the Presence ofAnti-Oxidant Agents

The objectives of these studies were to evaluate the sensitivity ofPeroxidase with Biotin-ASA-UP and ASA-UP, and to investigate the effectof various anti-oxidant agents on ASA-UP.

The materials used were Biotin (125 μg/ml), and ASA (125 μg/ml) inPBS-EDTA, pH 6.0; and ASA (125 μg/ml) in PBS-EDTA, pH 6.0. Results inFIG. 17 show that the Biotin-ASA-UP combination provides a sensitiveassay that can detect as low as 0.00625 pg sample. ASA-UP without HBAalso enables detection as low as 2 pg of HRPO.

Representative results of comparisons of the Raman-based assays appearin Tables 14-18. Raman Reagent A (increasing ASA from 100 to 250 or 500μg/ml), Reagent B, and Biotin-ASA provide ultra sensitive peroxidaseassays, compared to Reagent A-1 and Reagent C formulations. Raman-basedassays provide highly sensitive detection of Peroxidase in solution,which is shown graphically in FIG. 18.

Interestingly, ASA by itself provides very good sensitivity, which isincreased by the addition of CDMP, Biotin and even NAP. In reactionsbased on A-1 in which ascorbate and HBA were omitted, the limit ofdetection of peroxidase was 3.9 and 4.4 pg/ml when 500 μg/ml of ASA wasused and Raman signal analyzed with wave number 3,300^(cm−1) and SQR,respectively. When 750 μg/ml of ASA was used, the limit of detection was2.3 and 1.9 when the Raman signal was analyzed with wave number3,300^(cm−1) and SQR, respectively

Use of fresh HRPO, HPRO that is used within about three hours ofpreparation, results in greater sensitivity, and samples should not beused after storage, even at 2-8° C. overnight if greater sensitivity isrequired. The following tables (Tables. 14-18) summarize detectionlimits relevant to the preceding examples from representativeexperiments.

TABLE 14 SENSITIVITY OF RAMAN BASED ASSAY RELATIVE TO ABTS (SQR WITH3500-4000 CM⁻¹) Sample/ Reaction Lowest Limit of Sensitivity PeroxidaseVolume Detection (pg) for Relative Formulations Dilution Buffer (μl) 50μl Sample ABTS A-1 PBS with BSA 50/250 0.5 100 C-1 PBS with BSA 50/2500.1 500 A-2 PBS with BSA 50/250 0.05 1000 A-2 PBS with BSA, 50/2500.00625 8000 Fresh HRPO B-3 PBS with BSA 50/250 0.05 1000 B-3 PBS withBSA, 25/250 0.00625 8000 Fresh HRPO Biotin-ASA PBS with BSA, 25/2500.00625 8000 Fresh HRPO ASA-UP PBS with BSA, 25/250 2.0 25 Fresh HRPO

TABLE 15 DETECTION LIMITS WITH RAMAN REAGENT FORMULATIONS WITH HRPO INBSA DILUENT Increase in Sensitivity Peroxidase Sample/ from SingleFormulations Dilution Buffer Negative SQR Peak to SQR B-1 PBS with 0.1%5 pg 1 pg 5 times BSA B-2 PBS with 0.1% 1 pg 0.5 pg 2 times BSA B-3 PBSwith 0.1% 0.5 pg 0.05 10 times  BSA B-3 PBS with 0.1% 0.25 pg 0.00625 pg40 times  BSA. Fresh HRPO B-4 PBS with 0.1% 2.5 pg 0.5 pg 5 times BSAA-1 PBS with 0.1% 1 pg 0.5 pg 2 times BSA A-2 PBS with 0.1% 1 pg 0.05 pg20 times  BSA A-2 PBS with 0.1% 0.25 pg 0.00625 pg 40 times  BSA. FreshHRPO A-3 PBS with 0.1% 1 pg 1 pg No Change BSA C-2 PBS with 0.1% 0.5 pg0.1 pg 5 times BSA C-3 PBS with 0.1% 0.5 pg 0.25 pg 2 times BSA, FreshHRPO D-1 PBS with 0.1% 2 pg 0.5 pg 4 times BSA E-2 PBS with 0.1% 50 pgNA NA BSA

TABLE 16 DETECTION LIMITS WITH RAMAN REAGENT FORMULATIONS WITH HRPO INPBS DILUENT Increase in Sensitivity from Single Peroxidase Sample/ Peakto Formulations Dilution Buffer Negative SQR SQR A-2 PBS, pH 7.4 0.5 pg0.0125 pg 40 times B-3 PBS, pH 7.4 0.5 pg   0.5 pg None C-3 PBS, pH 7.4  1 pg 0.0125 pg 80 times A-2 PBS, pH 7.4, Fresh 2.5 pg  0.05 pg 50times B-3 PBS, pH 7.4, Fresh 0.25 pg   0.05 pg  5 times C-3 PBS, pH 7.4,Fresh 0.5 pg 0.0125 pg 40 times

TABLE 17 DETECTION LIMITS WITH COLORIMETRIC AND FLUOROGENIC REAGENTSLowest Limit of Sample/ Detection Time of Reaction (pg) PeroxidaseIncubation Volume for 50 μl Formulations Dilution Buffer (Minutes) (μl)Sample TMB PBS, pH 7.4 with 30 50/250 25 or w/o BSA ABTS PBS, pH 7.4with 30 50/250 50 or w/o BSA Amplex Red PBS, pH 7.4 with 30 400/800  25Fluorogenic or w/o BSA AnaSpec PBS, pH 7.4 with 30 400/800  12.5 ADHP orw/o BSA Fluorogenic A-1 PBS with BSA 30/30 50/250 0.5 A-2 PBS with BSA30/30 50/250 0.05 A-3 PBS with BSA 30/30 50/250 1 A-2 PBS with BSA,Fresh 30/30 50/250 0.00625 HRPO A-2 PBS, pH 7.4 30/30 50/250 0.0125 A-2PBS, pH 7.4, Fresh 30/30 50/250 0.05 HRPO B-1 PBS with BSA 30/30 50/2501 B-2 PBS with BSA 30/30 50/250 5 B-4 PBS with BSA 30/30 50/250 0.50 B-3PBS with BSA 30/30 50/250 0.05 B-3 PBS with BSA, Fresh 30/30 50/2500.00625 HRPO B-3 PBS, pH 7.4, Fresh 30/30 50/250 0.05 HRPO B-3 PBS, pH7.4 30/30 50/250 0.50 C-1 PBS with 0.1% BSA 30/30 50/250 0.10 C-3 PBSwith BSA, Fresh 30/30 50/250 0.25 HRPO C-3 PBS, pH 7.4 30/30 50/2500.0125 C-3 PBS, pH 7.4, Fresh 30/30 50/250 0.0125 HRPO Biotin-ASA PBS,pH 7.4, Fresh 30/30 50/250 0.00625 125/125 HRPO

Note that the Amplex Read Peroxidase assay is linear between 25 and 250pg/50 μl of sample (per vendor's claim) and the assay is able to detectas low as 1×10−5 U/ml. The Sigma HRPO used in the current study had anactivity of 1080 U/mg solid. On this basis, 1×10−5 U/ml HRPO isequivalent to 10 pg/ml (0.5 pg/50 μl).

Table 18 summarizes a representative comparison of Raman-based detectionand detection by absorbance, chemiluminescence, and fluorescence.

TABLE 18 SUMMARY OF COMPARATIVE DATA Limit of Dynamic range ReagentTechnique Detection (Peroxidase conc. in pg/ml) BASH-UP (SQR) Raman 3-6pg/mL   1,250 fold    4 to 5,000 TMB Detection (A₄₅₀) Absorbance  8pg/mL 125 fold  8 to 1,000 ABTS Detection Absorbance 32 pg/mL 156 fold32 to 5,000 (A₄₀₅) OPD Detection Absorbance 55 pg/mL  91 fold 55 to5,000 (A₄₉₂) LumiGLO Chemi- 11 pg/mL 455 fold 11 to 5,000 Detectionluminescence Amplex Red Fluorescence 257 pg/mL   91 fold 257 to 5,000 

The effect of various anti-oxidant agents on Raman-based detectionassays was examined. The effect of anti-oxidant agents on peroxidasereactions using 750 μg/ml ASA in representative experiments aresummarized in Table 19.

TABLE 19 EFFECTS OF ANTI-OXIDANTS Anti-Oxidant Agents Sodium 3,300 RamanN-Acetyl- Gallic Meta- Sodium Signal Ascorbate L-Cystine Melatonin Acidbisulfite Selenite Negative (0 pg/mL 953 1052 953 1031 978 903 HRPO)Negative + 411 677 965 1585 2453 966 Anti-Oxidant Positive (125 pg/mL2177 2369 3395 3022 2297 2887 HRPO) Positive + 751 1499 3198 2480 19202950 Anti-Oxidant Positive 1.8 2.2 3.3 1.6 1.97 3.1 Signal/Noise Ratio

Example 10 Immunoassays Using Raman-Based Detection

Raman-based methods were employed to the immunoassay formats availablefrom R&D Systems Inc. (D2050), BD Biosciences (5506111), BD Biosciences(557825), R&D Systems Inc. (DRT200), and BioCheck Inc (BC-1105). Theassay protocols were followed according to the manufacturer'sinstructions, with the exception that substrates producing Raman-activecompounds were substituted for TMB. The experiments using Raman-activecompounds were conducted as follows:

Reagent A

1. 5-Aminosalicylic Acid: 250 ug/mL

2. 2-Hydroxybenzyl Alcohol: 20 ug/mL

3. Ascorbic Acid: 0.2 ug/mL

The above three reagents were dissolved in 10 mM phosphate bufferedsaline with 1 mM EDTA, pH 6.0 (PBS-EDTA) and filtered through a sterile0.45 micron cellulose nitrate filter and was stored in an amber-coloredpolyethylene bottle at 2-8° C.

Reagent B

1. Urea-Peroxide: 1000 ug/mL which Contains 360 Ug/Ml Hydrogen Peroxide

The reagent was dissolved in 10 mM phosphate buffered saline with 2 mMEDTA, pH 6.0 (PBS-EDTA) and filtered through a sterile 0.45 microncellulose nitrate filter and was stored in an amber colored polyethylenebottle at 2-8 degree.

Raman Substrate

Raman substrate was prepared by mixing Reagent A and Reagent B in avolume ratio of 9:1 prior to use. The substrate should be used in thesame of preparation.

The results from representative experiments are summarized in Table 20.

TABLE 20 RAMAN-BASED IMMUNOASSAYS Limit of Detection Dynamic RangeAnalyte Raman TMB Mfg. Claim Raman Mfg. Claim Human IL-2 (R&D)   2 pg/mL 47 pg/mL 7 pg/mL   2-2,000  31-2,000 Human IL-2 (BD)   2 pg/mL 6.5pg/mL 4 pg/mL 2-500 7.8-500 C-Reactive Protein 2-4 μg/mL   20 μg/mL 4.2μg/mL   2-133 4.2-133 Tumor 0.3 pg/mL 0.3 pg/mL 0.6 pg/mL   0.3-500  7.8-500 Necrosis Factor Receptor II Human 0.5 ng/mL   3 ng/mL 1 ng/mL2-75   2-75 Cardiac Troponin I

Introduction of substrates producing Raman-active products into theHuman IL-2 assay resulted in an approximately 5-20 fold improvement inassay sensitivity. FIG. 19. The shift of the IL-2 dose response curve tothe left demonstrated in FIG. 19 exemplifies this improved sensitivity.

Example 11 Absorbance, Fluorescence, and Raman Detection of BASH-UP andOPD Reactions with HRPO

Studies using o-phenylenediamine as a peroxidase substrate revealed thatOPD produces a Raman signal that is peroxidase dependent, does notrequire addition of NaOH, and can be detected over a wide range of wavenumbers. The signal is more pronounced in the absence of NaOH, but ispresent in an altered form when the reaction is stopped with either NaOHor H₂SO₄.

Studies were done to evaluate the fluorescence and absorptioncharacteristics of Raman peroxidase reactions using o-phenylenediamine(OPD) and BASH-UP substrate solutions. The OPD and BASH-UP reactionswere prepared according to the following procedures:

OPD Protocol:

-   -   1. prepare OPD substrate solutions per SIGMAFAST™ OPD        instructions;    -   2. prepare HRPO peroxidase dilutions in buffer (PBS-BSA) to        4,000 pg/ml;    -   3. prepare the OPD/peroxide substrate solution (substrate        solution should be used within one hour of preparation);    -   4. add 250 μl diluted peroxidase sample to each reaction tube;    -   5. add 750 μl OPD/peroxide substrate to each tube; and    -   6. mix and incubate for 15 min in the dark at room temperature.

BASH-UP Protocol:

-   -   1. prepare the BASH-UP substrate solution (9:1 BASH to UP, v/v);    -   2. add 200 μl of diluted peroxidase dilution to each reaction        tube;    -   3. add 600 μl BASH-UP substrate solution to each tube;    -   4. mix and incubate for 30 min at room temperature;    -   5. add 200 μl of 0.5 N NaOH stop solution to each reaction tube;        and    -   6. mix and incubate for 30 min at room temperature.

Reactions with either BASH-UP, or OPD-peroxide reagents were performedon sample solutions containing either 0 or 2,000 pg/ml peroxidase asfollows:

OPD Reactions

-   -   1. Mix 250 μl of 2,000 pg/ml Peroxidase+750 μl OPD-peroxide        substrate solution;    -   2. Mix 250 μl of 1×PBS-BSA Buffer+750 μl OPD-peroxide substrate        solution;    -   3. Add peroxidase and allow reaction to proceed in the dark.    -   4. Read spectrum 30 min after the reaction time has expired.

BASH Reactions

-   -   1. 200 μl peroxidase (at 2,000 pg/ml conc.)+600 μl BASH-UP+200        μl 0.5 N NaOH    -   2. 200 μl of 1×PBS-BSA buffer+600 μl BASH-UP+200 μl 0.5 N NaOH    -   3. Add peroxidase and BASH, react 30 min, stop with NaOH.    -   4. Read spectrum 30 min after stopping the reaction.

Absorbance. Scans were performed with a Digilab Hitachi U-2800spectrophotometer and spectra were recorded using 0.750 ml of eachreaction sample using a single beam mode. The background sample (0 pg/mlperoxidase) was used as baseline. Spectra (340 to 650 nm; 1200 nm/minscan rate; 2 nm interval) are shown in FIGS. 20 A and 20 B. Theabsorption spectra of the BASH reaction was broad covering the visiblewavelength range (centered around 500 nm) lacking distinct peaksassociated with a unique absorbing species (FIG. 20 A). The absorptionspectra of the OPD reaction was more defined (FIG. 20 B), with a broadpeak near 440 nm (yellow wavelength range).

Fluorescence. Scans were performed with an Ocean Optics USB 2.0 FiberOptic lens with a 200 nm split and equipped with Spectrasuite software.Spectra were generated using excitation wavelengths of either 514 or 532nm. Emission spectra were collected using 12 second integration and abox width of 30. Emission spectra are shown in FIGS. 21 A-D. Thefluorescence emission spectra of both the negative (0 pg/ml peroxidase)and reactive (2,000 pg/ml peroxidase) BASH reactions were similar (FIGS.21 A and B), with a low level of inherent fluorescence. The OPD reactionfluorescence spectra were similar (FIGS. 22 A-D).

Raman. Spectra were collected on a Sword Diagnostics Raman Systems INCQE 65000 Raman Detector with a 532 nm laser; spectra of each reactionare shown in FIGS. 30 and 31. The BASH reaction resulted in a largeRaman signal (FIG. 23 A). This BASH reaction had a characteristic lightpink color associated with large peroxidase-containing samples. The OPDreaction also resulted in a large Raman signal (FIG. 23 B), and had acharacteristic yellow color also associated with largeperoxidase-containing samples. No increase in fluorescence signal wasobserved corresponding to the increase in Raman signal. In fact, thereappeared to be a slight decrease in fluorescence signal observed whenperoxidase was present. These observations were consistent at emissionwavelengths of 514 and 532 nm.

These results show that neither BASH reactions, nor OPD reactions whichresulted in large peroxidase dependent Raman signals, showed largeperoxidase dependent fluorescence signals. Therefore fluorescence cannotaccount for the Raman signals detected as a result of Peroxidaseactivity in the BASH or OPD reactions.

Example 12 Raman Sensitivity of OPD-Peroxidase Reactions andMeasurements of Enzyme Kinetics

Studies were done to evaluate and characterize the Raman signalassociated with the OPD-peroxidase reaction. The following procedure wasused for sample preparation:

OPD Reaction:

-   -   1. prepare OPD substrate solutions per SIGMAFAST™ OPD        instructions;    -   2. prepare 3M H₂SO₄ stop solution;    -   3. prepare peroxidase dilutions in buffer (PBS BSA) to 4,000        pg/ml;    -   4. prepare the OPD/peroxide substrate solution (substrate        solution should be used within one hour of preparation);    -   5. add 50 μl diluted peroxidase sample to each reaction tube;    -   6. add 150 μl OPD/peroxide substrate to each tube;    -   7. mix and incubate for 30 min in the dark at room temperature;    -   8. add 50 μl of 3M H₂SO₄ stop solution, 50 μl 0.5 N NaOH or 50        μl of 1×PBS-BSA solution to each reaction tube.

The following reaction mixtures were prepared in 5×60 mm cuvettes. Eachmixture was prepared and measured for 30 min prior to preparation of thenext reaction. Fresh OPD substrate was prepared each hour. The reactionsused are shown in Table 21:

TABLE 21 OPD REACTIONS Reaction No. Composition 1 50 μl peroxidase (at250 pg/ml conc.) + 150 μl OPD-peroxide substrate 2 50 μl peroxidase (at50 pg/ml conc.) + 150 μl OPD-peroxide substrate 3 50 μl peroxidase (at 5pg/ml conc.) + 150 μl OPD-peroxide substrate 4 50 μl of 1 × PBS-BSA +150 μl OPD-peroxide substrate

Kinetic studies were performed on each reaction, collecting Ramanspectra every 2 mins. FIGS. 24 A-E show spectra collected inapproximately 5-6 min intervals.

SQR analysis was applied to the collected spectra for the followingwavelength ranges: 2,000-2,500 cm⁻¹; 2,500-3,000 cm⁻¹; 3,000-3,500 cm⁻¹;and 3,500-4,000 cm⁻¹. The Raman kinetic plots of SQR spectra vs.OPD-peroxidase reaction time are shown in FIGS. 25 A-D. These resultsshow that kinetic rate information may be collected from single-tubeOPD-peroxidase reactions (collecting multiple Raman spectra during thecourse of a reaction from a single reaction tube).

The SOR values obtained after 30 minutes of reaction time were comparedto the estimated rate of reaction calculated by SQR, which revealed agood correlation between these values over a wide range of wave numbers.

1. A method for detecting the activity of at least one enzyme in asample comprising: a) preparing a mixture comprising the sample and: i.optionally at least one aromatic compound; ii. at least oneamine-containing compound; and iii. at least one electron-donatingcompound; b) incubating the mixture to form at least one Raman-activeproduct; and c) detecting the at least one Raman-active product withRaman spectroscopy.
 2. The method of claim 1, wherein the at least oneamine-containing compound is chosen from 4-aminoantipyrene and5-aminosalicyclic acid.
 3. The method of claim 1, wherein the at leastone aromatic compound is chosen from 2-hydroxybenzyl alcohol,4-chloro-3,5-dimethylphenol, 2-naphthol, 4-hydroxy-4-biphenyl-carboxylicacid, 5,7-dichloro-8-hydroxyquinoline, 4-chloro-1-naphthol, phenol, and4,5 dihydroxy-naphthalene-2,7-disulfonic acid.
 4. The method of claim 1,wherein the at least one amine-containing compound comprises:

wherein X is chosen from H, NH₂, Cl, Br, nitro, and benzyl, Y is chosenfrom H, Cl, Br, and nitro, and Z is chosen from H, benzyl, and NH₂. 5.The method of claim 1, wherein the at least one amine-containingcompound comprises:

wherein X is chosen from H, OH, Cl, Br, and nitro.
 6. The method ofclaim 1, wherein the at least one amine-containing compound comprises:

wherein X is selected from H, Br, Cl, and nitro.
 7. The method of claim1, wherein the amine-containing compound comprises:

wherein X, Y, and Z are chosen from H and NH₂.
 8. The method of claim 1,wherein the at least one aromatic compound comprises:

wherein W, X, Y, and Z are chosen from H and OH.
 9. The method of claim1, wherein the at least one aromatic compound comprises:

wherein X, Y, and Z are chosen from H and OH.
 10. The method of claim 1,wherein the at least one aromatic compound comprises:

wherein X and Y are chosen from H and OH.
 11. The method of claim 1,wherein the at least one aromatic compound comprises:

wherein X and Y are chosen from H and OH.
 12. The method of claim 1,wherein the at least one electron-donating compound is chosen from anorganic hydrogen peroxide, urea hydrogen peroxide, and hydrogen peroxide(H₂O₂).
 13. The method of claim 1, wherein the at least one enzyme is aperoxidase.
 14. The method of claim 1, wherein the at least one aromaticcompound is 2-hydroxybenzyl alcohol, the at least one amine containingcompound is 5-aminosalicyclic acid, the at least one electron-donatingcompound is urea hydrogen peroxide, and the at least one enzyme is aperoxidase.
 15. The method of claim 1, wherein step b) comprisesincubating the mixture in the presence of a base.
 16. The method ofclaim 1, wherein the Raman spectroscopy is resonance Raman Spectroscopy.17. A method for detecting the activity of at least one enzyme in asample comprising: a) preparing a mixture comprising the sample,5-aminosalicyclic acid, and a hydrogen peroxide; b) incubating themixture to form at least one Raman-active product; and c) detecting theat least one Raman-active product with Raman spectroscopy.
 18. Themethod of claim 17, wherein the mixture further comprises biotin. 19.The method of claim 17, wherein the hydrogen peroxide is urea hydrogenperoxide, and the enzyme is a peroxidase.
 20. A method for detecting theactivity of at least one enzyme in a sample comprising: a) preparing amixture comprising the sample, an aromatic amine chosen fromo-phenylenediamine, m-phenylenediamine, and p-phenylenediamine, and ahydrogen peroxide chosen from an aromatic hydrogen peroxide, ureahydrogen peroxide, and hydrogen peroxide (H₂O₂); b) incubating themixture to form at least one Raman-active product; and c) detecting theat least one Raman-active product with Raman spectroscopy.
 21. Themethod of claim 20, wherein the aromatic amine is o-phenylenediamine andthe hydrogen peroxide is urea hydrogen peroxide.
 22. A method fordetecting at least one target in a sample comprising: a) preparing amixture comprising the at least one target; b) incubating the mixturewith at least one ligand specific for the at least one target, whereinthe at least one ligand comprises an enzyme; c) providing to themixture: i. optionally at least one aromatic compound; ii. at least oneamine-containing compound; and iii. at least one electron-donatingcompound; d) incubating the mixture to form at least one Raman-activeproduct; and e) detecting the at least one Raman-active product withRaman spectroscopy.
 23. The method of claim 22, wherein the at least oneamine-containing compound is chosen from 4-aminoantipyrene and5-aminosalicyclic acid.
 24. The method of claim 22, wherein the at leastone aromatic compound is chosen from 2-hydroxybenzyl alcohol,4-chloro-3,5-dimethylphenol, 2-naphthol, 4-hydroxy-4-biphenyl-carboxylicacid, 5,7-dichloro-8-hydroxyquinoline, 4-chloro-1-naphthol, phenol, and4,5 dihydroxy-naphthalene-2,7-disulfonic acid.
 25. The method of claim22, wherein the at least one amine-containing compound is the compoundof claim
 4. 26. The method of claim 22, wherein the at least oneamine-containing compound is the compound of claim
 5. 27. The method ofclaim 22, wherein the at least one amine-containing compound is thecompound of claim
 6. 28. The method of claim 22, wherein the at leastone amine-containing compound is the compound of claim
 7. 29. The methodof claim 22, wherein the at least one aromatic compound is the compoundof claim
 8. 30. The method of claim 22, wherein the at least onearomatic compound is the compound of claim
 9. 31. The method of claim22, wherein the at least one aromatic compound is the compound of claim10.
 32. The method of claim 22, wherein the at least one aromaticcompound is the compound of claim
 11. 33. The method of claim 22,wherein the at least one electron-donating compound is chosen from anorganic hydrogen peroxide, urea hydrogen peroxide, and hydrogen peroxide(H₂O₂).
 34. The method of claim 22, wherein the enzyme is a peroxidase.35. The method of claim 22, wherein the at least one aromatic compoundis 2-hydroxybenzyl alcohol, the amine-containing compound is5-aminosalicyclic acid, the electron-donating compound is urea hydrogenperoxide, the at least one enzyme is a peroxidase, and the ligand is anantibody.
 36. The method of claim 22, wherein step b) comprisesincubating the mixture in the presence of a base.
 37. The method ofclaim 22, wherein the Raman spectroscopy is resonance RamanSpectroscopy.
 38. The method of claim 22, wherein the at least onetarget is an organism.
 39. The method of claim 38, wherein the organismis chosen from E. coli, Listeria, Salmonella, Vibrio, Camphelbacter,Staphylococcus, HIV, Hepatitis, Adenovirus, Rhino virus, and Humanpapilloma virus.
 40. The method of claim 22, wherein the target ischosen from a protein, amino acids, nucleic acids, nucleotides,carbohydrates, metabolites, hormones, and metabolic intermediates. 41.The method of claim 40, wherein the protein is chosen from IL-2,C-Reactive protein, Tumor Necrosis Factor Receptor II, and Human CardiacTroponin I.
 42. A method for detecting the activity of at least oneenzyme in a sample comprising: a) preparing a mixture comprising thesample and: i. optionally at least one aromatic compound; ii. at leastone amine-containing compound; and iii. at least one electron-donatingcompound; b) incubating the mixture to form at least one charge transfercomplex; and c) detecting the at least one charge transfer complex withRaman spectroscopy.
 43. A kit for detecting at least one enzyme activitycomprising: a) optionally, at least one aromatic compound; b) at leastone amine-containing compound; c) at least one electron-donatingcompound; and d) optionally, suitable buffers for the at least oneenzyme.
 44. The kit of claim 43, wherein the at least oneamine-containing compound is chosen from 4-aminoantipyrene,5-aminosalicyclic acid, and o-phenylenediamine, the at least oneoptional aromatic compound is chosen from 2-hydroxybenzyl alcohol,4-chloro-3,5-dimethylphenol, 2-naphthol, 4-hydroxy-4-biphenyl-carboxylicacid, 5,7-dichloro-8-hydroxyquinoline, 4-chloro-1-naphthol, phenol, and4,5 dihydroxy-naphthalene-2,7-disulfonic acid, and the at least oneelectron-donating compound is chosen from urea hydrogen peroxide andhydrogen peroxide.
 45. The kit of claim 43, wherein the at least onearomatic compound is chosen from 2-hydroxybenzyl alcohol,4-chloro-3,5-dimethylphenol, 2-naphthol, 4-hydroxy-4-biphenyl-carboxylicacid, 5,7-dichloro-8-hydroxyquinoline, 4-chloro-1-naphthol, phenol, and4,5 dihydroxy-naphthalene-2,7-disulfonic acid.
 46. The kit of claim 43,wherein the at least one amine-containing compound is the compound ofclaim
 4. 47. The kit of claim 43, wherein the at least oneamine-containing compound is the compound of claim
 5. 48. The kit ofclaim 43, wherein the at least one amine-containing compound is thecompound of claim
 6. 49. The kit of claim 43, wherein the at least oneamine-containing compound is the compound of claim
 7. 50. The kit ofclaim 43, wherein the at least one aromatic compound is the compound ofclaim
 8. 51. The kit of claim 43, wherein the at least one aromaticcompound is the compound of claim
 9. 52. The kit of claim 43, whereinthe at least one aromatic compound is the compound of claim
 10. 53. Thekit of claim 43, wherein the at least one aromatic compound is thecompound of claim
 11. 54. The kit of claim 43, wherein the at least onearomatic compound is an aromatic amine chosen from o-phenylenediamine,p-phenylenediamine, and m-phenylenediamine.